Effective modeling of conjunctive use of surface and subsurface water resources requires simulation of land use-based root zone and surface flow processes as well as groundwater flows, streamflows, and their interactions. Recently, two computer models developed for this purpose, the Integrated Water Flow Model (IWFM) from the California Department of Water Resources and the MODFLOW with Farm Process (MF-FMP) from the US Geological Survey, have been applied to complex basins such as the Central Valley of California. As both IWFM and MFFMP are publicly available for download and can be applied to other basins, there is a need to objectively compare the main approaches and features used in both models. This paper compares the concepts, as well as the method and simulation features of each hydrologic model pertaining to groundwater, surface water, and landscape processes. The comparison is focused on the integrated simulation of water demand and supply, water use, and the flow between coupled hydrologic processes. The differences in the capabilities and features of these two models could affect the outcome and types of water resource problems that can be simulated.